Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1130921 original size:22 final size:22
Alignment explanation
Indices: 1130896--1131057 Score: 90
Period size: 22 Copynumber: 6.5 Consensus size: 22
1130886 TTAAAATAAA
* *
1130896 TTATTATAAAATATATATTGAT
1 TTATTTTAAAATATAGATTGAT
1130918 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
*
1130940 TTATTTTAAATAATTTATTAGTATAGATT
1 TTATTTT-AA-AA--TA-TAG-ATTGA-T
*
1130969 GATTTATTTTAAAATATGGATTGAT
1 ---TTATTTTAAAATATAGATTGAT
*
1130994 TTATTTTAAATAATTTATTAGTATAGATT
1 TTATTTT-AA-AA--TA-TAG-ATTGA-T
*
1131023 GATTTATTTTAAAATATAGATTAAT
1 ---TTATTTTAAAATATAGATTGAT
1131048 TTATTTTAAA
1 TTATTTTAAA
1131058 TAATTTATTA
Statistics
Matches: 111, Mismatches: 9, Indels: 40
0.69 0.06 0.25
Matches are distributed among these distances:
22 44 0.40
23 4 0.04
24 4 0.04
25 2 0.02
26 11 0.10
27 10 0.09
28 12 0.11
29 2 0.02
30 4 0.04
31 4 0.04
32 14 0.13
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATAGATTGAT
Found at i:1130967 original size:32 final size:32
Alignment explanation
Indices: 1130929--1131287 Score: 238
Period size: 32 Copynumber: 11.7 Consensus size: 32
1130919 TATTTTAAAA
1130929 TATAGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
1130961 TATAGATTGATTTATTTT-AA-AA--TA-T-G
1 TATAGATTGATTTATTTTAAATAATTTATTAG
1130987 ----GATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
1131015 TATAGATTGATTTA-TTT---TAA---A--A-
1 TATAGATTGATTTATTTTAAATAATTTATTAG
*
1131037 TATAGATTAATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
**
1131069 TAT-GAATTGATTTATTTTAAA-ATATGGATT-G
1 TATAG-ATTGATTTATTTTAAATA-ATTTATTAG
** * *
1131100 -ATTTATT-ATTCTAGTTGTATAGATTGATTTATT--
1 TATAGATTGATT-TA-TT-T-TA-AATAATTTATTAG
* * * * *
1131133 T-TA-AATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATAGATTGATTTATT--T-T-AAATAATTTA--TT--AG
*
1131171 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
1131203 TAT-GAATTGATTTATTTTAAATAATTTATTAG
1 TATAG-ATTGATTTATTTTAAATAATTTATTAG
*
1131235 TATAGATTGATTTATTTTAAATAATTTATTTG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
1131267 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
1131288 ATATGAATTG
Statistics
Matches: 266, Mismatches: 18, Indels: 86
0.72 0.05 0.23
Matches are distributed among these distances:
22 27 0.10
23 6 0.02
24 2 0.01
25 1 0.00
26 6 0.02
27 2 0.01
28 6 0.02
29 4 0.02
30 9 0.03
31 14 0.05
32 150 0.56
33 8 0.03
34 10 0.04
36 8 0.03
37 1 0.00
38 2 0.01
39 1 0.00
40 9 0.03
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
TATAGATTGATTTATTTTAAATAATTTATTAG
Found at i:1130974 original size:54 final size:54
Alignment explanation
Indices: 1130907--1131399 Score: 419
Period size: 54 Copynumber: 9.0 Consensus size: 54
1130897 TATTATAAAA
*
1130907 TATATATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAG
*
1130961 TATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAG
*
1131015 TATAGATTGATTTATTTTAAAATATAGATTAATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAG
* *
1131069 TAT-GAATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TCTAGTT-G
1 TATAG-ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTAG
* * * * * *
1131117 TATAGATTGATTTATTTT--AA-ATA-ATTTA-TTAGTATGAATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTA-TTTTAAATAATTTA--TT--AG
*
1131171 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTT--A-AA---A-TA-TA-G-ATTGATTTATTTTAAATAATTTATTAG
* * * * * *
1131235 TATAGATTGATTTATTTT--AA-ATA-ATTTATTT-GTATAGATTGATTTATTTTAA
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTA-AATAATTTA--TTAG
* **
1131287 AATATGAATTGATTTATTATTATAGTTGTATAGATTGATTTATTTTAAATAATTTATTAG
1 TATA-G-ATTGATTTATT-TTA-A--AATATAGATTGATTTATTTTAAATAATTTATTAG
* *
1131347 TATAGATTAATTTATTTTAAAATATAAATTGATTTATTTTAAATAATTTATTA
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTA
1131400 TTGTAATTGT
Statistics
Matches: 354, Mismatches: 42, Indels: 86
0.73 0.09 0.18
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
45 2 0.01
46 3 0.01
48 21 0.06
49 6 0.02
50 19 0.05
51 2 0.01
52 8 0.02
53 4 0.01
54 195 0.55
55 2 0.01
56 2 0.01
57 3 0.01
58 10 0.03
59 3 0.01
60 6 0.02
61 3 0.01
62 15 0.04
63 3 0.01
64 19 0.05
65 2 0.01
66 2 0.01
68 14 0.04
69 3 0.01
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (54 bp):
TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAG
Found at i:1131133 original size:80 final size:83
Alignment explanation
Indices: 1131037--1131255 Score: 324
Period size: 80 Copynumber: 2.6 Consensus size: 83
1131027 TATTTTAAAA
*
1131037 TATAGATTAATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1131102 TTA-TT-AT-TCTAGTT-G
66 TTATTTAATATCTA-TTAG
1131117 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
1131182 TTATTTTAAATAATTTATTAG
66 TTA-TTT-AAT-ATCTATTAG
1131203 TAT-GAATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAA
1 TATAG-ATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAA
1131256 TAATTTATTT
Statistics
Matches: 128, Mismatches: 2, Indels: 12
0.90 0.01 0.08
Matches are distributed among these distances:
80 67 0.52
82 2 0.02
84 2 0.02
85 4 0.03
86 53 0.41
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (83 bp):
TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTTAATATCTATTAG
Found at i:1131160 original size:134 final size:117
Alignment explanation
Indices: 1131116--1131367 Score: 376
Period size: 118 Copynumber: 2.2 Consensus size: 117
1131106 TATTCTAGTT
1131116 GTATAGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTG
1 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATAT-GATTG
1131180 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTA
64 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTA
*
1131234 GTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGAATTGA
1 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG-ATTGA
* *
1131299 TTTATTATT--AT-AGTT-GTA-TA-G-ATTGATTTATTTTAAATAATTTATTA
65 TTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTA
*
1131346 GTATAGATTAATTTATTTTAAA
1 GTATAGATTGATTTATTTTAAA
1131368 ATATAAATTG
Statistics
Matches: 127, Mismatches: 4, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
112 47 0.37
113 1 0.01
114 2 0.02
115 2 0.02
116 3 0.02
117 3 0.02
118 66 0.52
119 3 0.02
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (117 bp):
GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATTGAT
TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:1131174 original size:22 final size:22
Alignment explanation
Indices: 1131149--1131191 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131139 AATTTATTAG
1131149 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1131171 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1131192 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1131199 original size:14 final size:14
Alignment explanation
Indices: 1131180--1131265 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 14
1131170 ATATGGATTG
1131180 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1131194 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1131212 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1131226 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
1131244 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1131258 ATTTATTT
1 ATTTATTT
1131266 GTATAGATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
14 27 0.48
15 3 0.05
16 4 0.07
17 3 0.05
18 19 0.34
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1131342 original size:80 final size:80
Alignment explanation
Indices: 1131234--1131384 Score: 275
Period size: 80 Copynumber: 1.9 Consensus size: 80
1131224 TAATTTATTA
* * *
1131234 GTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGAATTGA
1 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTGA
1131299 TTTATTATTATAGTT
66 TTTATTATTATAGTT
1131314 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTGA
1 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTGA
1131379 TTTATT
66 TTTATT
1131385 TTAAATAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (80 bp):
GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTGA
TTTATTATTATAGTT
Found at i:1131372 original size:22 final size:22
Alignment explanation
Indices: 1131347--1131389 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131337 AATTTATTAG
*
1131347 TATAGATTAATTTATTTTAAAA
1 TATAAATTAATTTATTTTAAAA
*
1131369 TATAAATTGATTTATTTTAAA
1 TATAAATTAATTTATTTTAAA
1131390 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TATAAATTAATTTATTTTAAAA
Found at i:1131382 original size:40 final size:40
Alignment explanation
Indices: 1131258--1131384 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 40
1131248 ATTTTAAATA
* * *
1131258 ATTTATTTGTATAGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTG
* * * * * *
1131298 ATTTATTATTATAGTTGTATAGATTGA-TTT--ATTTTAAA-TA
1 ATTTATTAGTATAG--AT-TA-ATTTATTTTAAAATATAAATTG
1131338 ATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTG
1 ATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTG
1131378 ATTTATT
1 ATTTATT
1131385 TTAAATAATT
Statistics
Matches: 64, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
36 4 0.06
37 5 0.08
38 1 0.02
39 6 0.09
40 34 0.53
41 5 0.08
42 1 0.02
43 4 0.06
44 4 0.06
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (40 bp):
ATTTATTAGTATAGATTAATTTATTTTAAAATATAAATTG
Found at i:1131471 original size:31 final size:31
Alignment explanation
Indices: 1131413--1131472 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1131403 TAATTGTATG
* ***
1131413 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATCTCAATATAACAAAACTAA
*
1131444 AATTATTTAAATCTCAGTATAACAAAACT
1 AATTATTTAAATCTCAATATAACAAAACT
1131473 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.38
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATAACAAAACTAA
Found at i:1139200 original size:22 final size:23
Alignment explanation
Indices: 1139152--1139195 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1139142 GACCGATTGT
**
1139152 TCTTTTTTTTCAACCCAACCCCA
1 TCTTTTTCCTCAACCCAACCCCA
1139175 TCTTTTTCCTCAACCCAACCC
1 TCTTTTTCCTCAACCCAACCC
1139196 GTCTTCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.36
Consensus pattern (23 bp):
TCTTTTTCCTCAACCCAACCCCA
Found at i:1142344 original size:3 final size:3
Alignment explanation
Indices: 1142336--1142387 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
1142326 CCTTCAATAA
1142336 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1142383 ATT AT
1 ATT AT
1142388 CTTCTTTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1143748 original size:59 final size:60
Alignment explanation
Indices: 1143677--1143791 Score: 214
Period size: 59 Copynumber: 1.9 Consensus size: 60
1143667 AAGATTTTAA
1143677 TTTAAATATTTTTATATGTATAAAATATATAAATACTCTTACGGTATATTAGTTTTCAAT
1 TTTAAATATTTTTATATGTATAAAATATATAAATACTCTTACGGTATATTAGTTTTCAAT
*
1143737 TTTAAAT-TTTTTATATGTATAAAATATATAAATACTCTTATGGTATATTAGTTTT
1 TTTAAATATTTTTATATGTATAAAATATATAAATACTCTTACGGTATATTAGTTTT
1143792 GTGTCTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 47 0.87
60 7 0.13
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.50
Consensus pattern (60 bp):
TTTAAATATTTTTATATGTATAAAATATATAAATACTCTTACGGTATATTAGTTTTCAAT
Found at i:1144253 original size:26 final size:28
Alignment explanation
Indices: 1144224--1144281 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
1144214 TAGATTATAA
*
1144224 TAAAGTTTTTC-AAAG-TTTGGATTTTT-
1 TAAAGATTTTCAAAAGATTTGG-TTTTTC
1144250 TAAAGATTTTCAAAAGATTTGGTTTTTC
1 TAAAGATTTTCAAAAGATTTGGTTTTTC
1144278 TAAA
1 TAAA
1144282 AATAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 10 0.36
27 9 0.32
28 9 0.32
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (28 bp):
TAAAGATTTTCAAAAGATTTGGTTTTTC
Found at i:1147881 original size:157 final size:150
Alignment explanation
Indices: 1147605--1147906 Score: 516
Period size: 157 Copynumber: 2.0 Consensus size: 150
1147595 AGCTTTGGTC
*
1147605 TGGTTCATTACCACACAACGGAATTAATAATTAAGAGTGGTGCATGCAAGGGGACCCACGTGGGT
1 TGGTTCATTACCACACAACGGAATTAATAATTAAGAGTGGTGCATGCAAGGGCACCCACGTGGGT
1147670 TATGGTAATGCCCCCACACTAATTTACTTGCAAAATGGGGTTATGATTTCTTAAAAGGAAAATCA
66 TATGGTAATGCCCCCACACTAATTTACTTGCAAAATGGGGTTATGATTTCTTAAAAGGAAAATCA
1147735 TGTGGGTGGTGATTTGTCTT
131 TGTGGGTGGTGATTTGTCTT
1147755 TGGTTCATTACCACATACAACCGGAATTAATAATTAAGAGTGGTGCATGCAAGGGACACTCCACG
1 TGGTTCATTACCAC--ACAA-CGGAATTAATAATTAAGAGTGGTGCATGCAAGGG-CAC-CCACG
1147820 TGGGTTATGTGGTAATGCCCCACACACTAA-TTACTTGCAAAATGGGGTTATGATTTCTTAAAAG
61 TGGGTTA--TGGTAATGCCCC-CACACTAATTTACTTGCAAAATGGGGTTATGATTTCTTAAAAG
1147884 GAAAATCATGTGGGTGGTGATTT
123 GAAAATCATGTGGGTGGTGATTT
1147907 AAAAAGAAAA
Statistics
Matches: 143, Mismatches: 1, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
150 14 0.10
152 4 0.03
153 34 0.24
154 2 0.01
155 12 0.08
157 69 0.48
158 8 0.06
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (150 bp):
TGGTTCATTACCACACAACGGAATTAATAATTAAGAGTGGTGCATGCAAGGGCACCCACGTGGGT
TATGGTAATGCCCCCACACTAATTTACTTGCAAAATGGGGTTATGATTTCTTAAAAGGAAAATCA
TGTGGGTGGTGATTTGTCTT
Found at i:1150056 original size:48 final size:48
Alignment explanation
Indices: 1150004--1150132 Score: 131
Period size: 48 Copynumber: 2.7 Consensus size: 48
1149994 AATATTTTAC
*
1150004 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
1150052 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
1150100 CTG-TTACTT-GACCTGATTTCTGATATGATACTT
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTT
1150133 AACCTGATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
47 5 0.08
48 57 0.86
49 3 0.05
50 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:1150142 original size:24 final size:24
Alignment explanation
Indices: 1150021--1150132 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
1150011 TCGATTTGAT
1150021 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
1150045 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
1150069 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
1150093 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
1150116 TTTCTGATATGATACTT
1 -TTCTGATCTGATACTT
1150133 AACCTGATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1155792 original size:48 final size:48
Alignment explanation
Indices: 1155740--1155868 Score: 131
Period size: 48 Copynumber: 2.7 Consensus size: 48
1155730 AATATTTTAC
*
1155740 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
1155788 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
1155836 CTG-TTACTT-GACCTGATTTCTGATATGATACTT
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTT
1155869 AACCTGATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
47 5 0.08
48 57 0.86
49 3 0.05
50 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:1155878 original size:24 final size:24
Alignment explanation
Indices: 1155757--1155868 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
1155747 TCGATTTGAT
1155757 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
1155781 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
1155805 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
1155829 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
1155852 TTTCTGATATGATACTT
1 -TTCTGATCTGATACTT
1155869 AACCTGATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1158863 original size:3 final size:3
Alignment explanation
Indices: 1158855--1158913 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
1158845 TTTTTACCCA
*
1158855 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1158903 TAT TAT TAT TA
1 TAT TAT TAT TA
1158914 AATATATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1160373 original size:16 final size:17
Alignment explanation
Indices: 1160341--1160376 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1160331 TAAAATATAA
*
1160341 TAAATAAATATTTATTT
1 TAAATAAATAATTATTT
1160358 TAAATAAA-AATTATTT
1 TAAATAAATAATTATTT
1160374 TAA
1 TAA
1160377 TATTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATAAATAATTATTT
Found at i:1161062 original size:17 final size:17
Alignment explanation
Indices: 1161032--1161076 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1161022 TTTAATTTTT
* *
1161032 AATTTTTTTCTTTTCAA
1 AATTTTTATATTTTCAA
*
1161049 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
1161066 AATATTTATAT
1 AATTTTTATAT
1161077 GTTTTATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:1171728 original size:1 final size:1
Alignment explanation
Indices: 1171722--1171794 Score: 83
Period size: 1 Copynumber: 73.0 Consensus size: 1
1171712 ATGCTTGATG
* * * * * *
1171722 AAAAAAAAGAAAAAAAGAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1171787 AAGAAAAA
1 AAAAAAAA
1171795 GGGGGGTCAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:1171745 original size:11 final size:11
Alignment explanation
Indices: 1171722--1171793 Score: 103
Period size: 11 Copynumber: 6.5 Consensus size: 11
1171712 ATGCTTGATG
*
1171722 AAAAAA-AAGA
1 AAAAAAGAAAA
1171732 AAAAAAGAAAA
1 AAAAAAGAAAA
1171743 AAAAAAGAAAA
1 AAAAAAGAAAA
1171754 AAAAAAGAAAA
1 AAAAAAGAAAA
1171765 AAAAAA-AGAAA
1 AAAAAAGA-AAA
1171776 AAAAAAGAAAA
1 AAAAAAGAAAA
1171787 AAGAAAA
1 AA-AAAA
1171794 AGGGGGGTCA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
10 7 0.12
11 45 0.79
12 5 0.09
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1172161 original size:17 final size:17
Alignment explanation
Indices: 1172124--1172167 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1172114 CTATTTCAAG
*
1172124 TTCAATTTA-TTTGAGA
1 TTCAATTTATTTTGAAA
*
1172140 TTCAATTTATTTTTAAA
1 TTCAATTTATTTTGAAA
1172157 TTCAATTTATT
1 TTCAATTTATT
1172168 CTTTTCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:1173069 original size:83 final size:83
Alignment explanation
Indices: 1172930--1173492 Score: 914
Period size: 83 Copynumber: 6.7 Consensus size: 83
1172920 AAACATTAAC
* * *
1172930 TAGAAGATGAATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
1 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1172994 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
* * *
1173013 TAGAAGATGAATTTGCCCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1173078 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
1173096 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1173161 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
1173179 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1173243 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
1173262 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1173327 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* ** *
1173345 TAGAGGATGAATGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
1 TAGAAGATGAATTTG-C-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
1173410 ACAGAACCAATCATTGAATT
64 ACAGAACCAATCATTGAATT
* * *** *
1173430 TATAGGATGAAGAAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGAAGATGAATTTG-C-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1173493 TGGTATGAAC
Statistics
Matches: 462, Mismatches: 13, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
82 5 0.01
83 326 0.71
84 5 0.01
85 126 0.27
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (83 bp):
TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAACCAATCATTGAATT
Found at i:1174424 original size:113 final size:113
Alignment explanation
Indices: 1174226--1174659 Score: 726
Period size: 113 Copynumber: 3.8 Consensus size: 113
1174216 CAAATCTATT
* *
1174226 ATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGA
1 ATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
1174290 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
65 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
1174339 ATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 ATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1174404 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
66 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
*
1174452 ATTTAATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 ATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * *
1174517 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATC
66 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
* * *
1174565 AAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 -ATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* * *
1174630 AGAAGTTCATAATAAGAAGAACTTGTTCAA
65 AGAAATTCATAATGAGAAGAATTTGTTCAA
1174660 TAATTCTATC
Statistics
Matches: 305, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
112 2 0.01
113 216 0.71
114 87 0.29
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (113 bp):
ATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
Found at i:1174984 original size:3 final size:3
Alignment explanation
Indices: 1174976--1175049 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
1174966 TTTTTACCCA
1174976 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1175024 TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1175050 AATATATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1175815 original size:30 final size:29
Alignment explanation
Indices: 1175781--1175839 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1175771 TAAAATAATA
*
1175781 TATTTAGGATAAATAATAGATTTAATCCTT
1 TATTTAGAATAAATAATA-ATTTAATCCTT
** *
1175811 TATTTTTAATAAATAATATTTTAATCCTT
1 TATTTAGAATAAATAATAATTTAATCCTT
1175840 AGTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (29 bp):
TATTTAGAATAAATAATAATTTAATCCTT
Found at i:1176131 original size:16 final size:17
Alignment explanation
Indices: 1176099--1176134 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1176089 AAATATATAA
*
1176099 TAAATAAATATTTATTT
1 TAAATAAATAATTATTT
1176116 TAAATAAA-AATTATTT
1 TAAATAAATAATTATTT
1176132 TAA
1 TAA
1176135 TATTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATAAATAATTATTT
Found at i:1189307 original size:20 final size:20
Alignment explanation
Indices: 1189265--1189312 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1189255 ACCCTTAGAA
*
1189265 AAAAAATAAAAAAAAAGGTC
1 AAAAAATAAAAAAAAAGATC
1189285 AAAAAATAAAAAAAAA-ATAC
1 AAAAAATAAAAAAAAAGAT-C
1189305 AAAAAATA
1 AAAAAATA
1189313 TATAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.10
Consensus pattern (20 bp):
AAAAAATAAAAAAAAAGATC
Found at i:1189602 original size:12 final size:12
Alignment explanation
Indices: 1189579--1189612 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1189569 AAATATTAAT
1189579 TTTTTTATATAAA
1 TTTTTTA-ATAAA
1189592 TTTTTTAATAAA
1 TTTTTTAATAAA
*
1189604 GTTTTTAAT
1 TTTTTTAAT
1189613 TTTTGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTTTAATAAA
Found at i:1191164 original size:25 final size:25
Alignment explanation
Indices: 1191136--1191200 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
1191126 GCTATAATTT
*
1191136 TAAATTAAACTAATAATAAAATATA
1 TAAATTAAACTAATAATAAAAAATA
* **
1191161 TAAAATAAGTTAAT-ATAAAAAATA
1 TAAATTAAACTAATAATAAAAAATA
**
1191185 TTTATTAAACTTAATA
1 TAAATTAAAC-TAATA
1191201 TATGTGTGTG
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATTAAACTAATAATAAAAAATA
Found at i:1203119 original size:25 final size:25
Alignment explanation
Indices: 1203082--1203143 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
1203072 AAATAATATA
1203082 AAAT-ATAAAAACACTAAAAAATTC
1 AAATAATAAAAACACTAAAAAATTC
*
1203106 AAATAATAAAAACACTAGAAAATTC
1 AAATAATAAAAACACTAAAAAATTC
1203131 AAATAATATAAAA
1 AAATAATA-AAAA
1203144 TATAAAGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 4 0.11
25 27 0.77
26 4 0.11
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.21
Consensus pattern (25 bp):
AAATAATAAAAACACTAAAAAATTC
Found at i:1203185 original size:18 final size:18
Alignment explanation
Indices: 1203164--1203209 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1203154 AACTATTTTT
*
1203164 TAAAATTTAATA-AAAAGA
1 TAAAAATTAATATAAAA-A
*
1203182 TAAAAAATAATATAAAAA
1 TAAAAATTAATATAAAAA
1203200 TAAAAATTAA
1 TAAAAATTAA
1203210 CCGACTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAATTAATATAAAAA
Found at i:1209018 original size:29 final size:30
Alignment explanation
Indices: 1208965--1209026 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
1208955 AAAAAATTAA
*
1208965 AATAAAATAATATTAATAATGTT-AAGACT
1 AATAAAAAAATATTAATAATGTTAAAGACT
1208994 AATAAAAAAATATTTTAA-AAT-TTAAAGACT
1 AATAAAAAAATA--TTAATAATGTTAAAGACT
1209024 AAT
1 AAT
1209027 CTTAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 13 0.45
30 12 0.41
31 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (30 bp):
AATAAAAAAATATTAATAATGTTAAAGACT
Found at i:1219950 original size:24 final size:23
Alignment explanation
Indices: 1219906--1219950 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1219896 TTAATTTAAG
* *
1219906 AAAAATAATATATATTTAATGTA
1 AAAAATAATATATACTGAATGTA
*
1219929 AAAAATCATATGATACTGAATG
1 AAAAATAATAT-ATACTGAATG
1219951 GTTGCTGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (23 bp):
AAAAATAATATATACTGAATGTA
Found at i:1232432 original size:116 final size:116
Alignment explanation
Indices: 1232308--1232534 Score: 294
Period size: 116 Copynumber: 2.0 Consensus size: 116
1232298 AAAAACATTA
* * *
1232308 TTAAATTTAATTCAAAATTGAATGAATAAATAAGA-AAATGGAAAAAGAGAGTCAAAAACTAAAA
1 TTAAATTTAATTCAAAATTGAATG-ATAAATAAGAGAAACGAAAAAAGAGAGTAAAAAACTAAAA
* * *
1232372 TTTAATGAACTTATAAAAATTAGGGGACTTAAATAGAAATATAAAAATTTGG
65 TTTAATGAAATTATAAAAATTAAGGGACCTAAATAGAAATATAAAAATTTGG
* * * * **
1232424 TTAAATTTAATTCAAAATTGGATGATTAATAAGAGAAACGAAAAAAGAGGGTAAAAAATTAATTT
1 TTAAATTTAATTCAAAATTGAATGATAAATAAGAGAAACGAAAAAAGAGAGTAAAAAACTAAAAT
* * * *
1232489 TTTATGAAATTATAAAAATTAAGGGTCCTAATTATAAATATAAAAA
66 TTAATGAAATTATAAAAATTAAGGGACCTAAATAGAAATATAAAAA
1232535 ATTGAAGACT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
115 9 0.10
116 85 0.90
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.30
Consensus pattern (116 bp):
TTAAATTTAATTCAAAATTGAATGATAAATAAGAGAAACGAAAAAAGAGAGTAAAAAACTAAAAT
TTAATGAAATTATAAAAATTAAGGGACCTAAATAGAAATATAAAAATTTGG
Found at i:1232809 original size:29 final size:30
Alignment explanation
Indices: 1232776--1232834 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1232766 TGATTTTTTA
1232776 ATAATAGTTAT-ATCTTAAATATCTAAATT
1 ATAATAGTTATAATCTTAAATATCTAAATT
* *
1232805 ATAATATTTATAATGTTAAATATCTAAATT
1 ATAATAGTTATAATCTTAAATATCTAAATT
1232835 TATATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (30 bp):
ATAATAGTTATAATCTTAAATATCTAAATT
Found at i:1242948 original size:16 final size:16
Alignment explanation
Indices: 1242927--1242963 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1242917 AATCCTTAAT
1242927 AGCATAAAATTAGCTA
1 AGCATAAAATTAGCTA
1242943 AGCATAAAATTAGCTA
1 AGCATAAAATTAGCTA
1242959 AGCAT
1 AGCAT
1242964 TCATCCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (16 bp):
AGCATAAAATTAGCTA
Found at i:1247437 original size:3 final size:3
Alignment explanation
Indices: 1247429--1247460 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1247419 GAGTGATTTC
*
1247429 GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1247461 GCTAATGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:1252687 original size:88 final size:88
Alignment explanation
Indices: 1252590--1252766 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
1252580 ATTTTTGTTT
1252590 TAATTTTTTTCAATTTGTTCACTTGACTATTTAAGTTATATCAATCAAGTCATTTACTGTTAACA
1 TAATTTTTTTCAATTTGTTCACTTGACTATTTAAGTTATATCAATCAAGTCATTTACTGTTAACA
*
1252655 TTTGACAGAAATTTGAGTTGATG
66 TTTGACAAAAATTTGAGTTGATG
*
1252678 TAATTTTTTTCAATTTGTTCACTTGACTATTTAAGTTATATCAATTAAGTCATTTACTGTTAACA
1 TAATTTTTTTCAATTTGTTCACTTGACTATTTAAGTTATATCAATCAAGTCATTTACTGTTAACA
1252743 TTTGACAAAAATTTGAGTTGATG
66 TTTGACAAAAATTTGAGTTGATG
1252766 T
1 T
1252767 GACATTTAAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (88 bp):
TAATTTTTTTCAATTTGTTCACTTGACTATTTAAGTTATATCAATCAAGTCATTTACTGTTAACA
TTTGACAAAAATTTGAGTTGATG
Found at i:1257679 original size:16 final size:16
Alignment explanation
Indices: 1257656--1257711 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1257646 CTTACTTTCG
1257656 GGTT-GGGTTAATTTT
1 GGTTCGGGTTAATTTT
* **
1257671 GGTTTGGGTTGCTTTCT
1 GGTTCGGGTTAATTT-T
*
1257688 -GTTCGAGTTAATTTT
1 GGTTCGGGTTAATTTT
1257703 GGTTCGGGT
1 GGTTCGGGT
1257712 CAAGCTAGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 5 0.16
16 25 0.81
17 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.34, T:0.50
Consensus pattern (16 bp):
GGTTCGGGTTAATTTT
Found at i:1258158 original size:21 final size:19
Alignment explanation
Indices: 1258134--1258183 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1258124 ACTACTCAAC
*
1258134 TTATATATTTTATATATTTAT
1 TTATATATTTTA-AT-TTAAT
1258155 TTAT-TATTTTAATTTAAT
1 TTATATATTTTAATTTAAT
1258173 TTATTATATTT
1 TTA-TATATTT
1258184 AACCCTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
20 12 0.46
21 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTAATTTAAT
Found at i:1259638 original size:21 final size:20
Alignment explanation
Indices: 1259610--1259674 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1259600 ATTTTTCAAA
1259610 GAAA-CATTTACCAAACTTT
1 GAAACCATTTACCAAACTTT
*
1259629 GAAAACCATTT-TCAAA----
1 G-AAACCATTTACCAAACTTT
1259645 GAAA-CATTTACCAAACTTT
1 GAAACCATTTACCAAACTTT
1259664 GTAAACCATTT
1 G-AAACCATTT
1259675 TTTTCAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 2 0.06
20 10 0.29
21 10 0.29
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (20 bp):
GAAACCATTTACCAAACTTT
Found at i:1259648 original size:35 final size:35
Alignment explanation
Indices: 1259566--1259675 Score: 159
Period size: 35 Copynumber: 3.1 Consensus size: 35
1259556 CATTATCATT
* * *
1259566 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
1259601 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
*
1259637 TTTTCAAAGAAACATTTACCAAACTTTGTAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1259672 TTTT
1 TTTT
1259676 TTTCAAAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 38 0.55
36 11 0.16
37 20 0.29
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1263826 original size:16 final size:16
Alignment explanation
Indices: 1263802--1263835 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1263792 TATTACCGAC
*
1263802 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1263818 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1263834 CG
1 CG
1263836 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1264304 original size:37 final size:36
Alignment explanation
Indices: 1264245--1264364 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
1264235 ATTCAATTAT
* *
1264245 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
1264281 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
1264317 CA-TATTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1264352 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1264365 TTGGTTACTA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1273137 original size:16 final size:16
Alignment explanation
Indices: 1273116--1273150 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1273106 AAATCAATGC
1273116 TATATATATGTGTATA
1 TATATATATGTGTATA
* *
1273132 TATATATGTGTGTGTA
1 TATATATATGTGTATA
1273148 TAT
1 TAT
1273151 GTTGGTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (16 bp):
TATATATATGTGTATA
Found at i:1273150 original size:14 final size:14
Alignment explanation
Indices: 1273116--1273142 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1273106 AAATCAATGC
1273116 TATATATATGTGTA
1 TATATATATGTGTA
1273130 TATATATATGTGT
1 TATATATATGTGT
1273143 GTGTATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TATATATATGTGTA
Found at i:1280313 original size:12 final size:12
Alignment explanation
Indices: 1280296--1280330 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1280286 ATTTCAAGTT
1280296 TAAATATTTTTA
1 TAAATATTTTTA
1280308 TAAATATTTTTA
1 TAAATATTTTTA
*
1280320 AATAATATTTT
1 TA-AATATTTT
1280331 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:1293304 original size:147 final size:153
Alignment explanation
Indices: 1293064--1293366 Score: 519
Period size: 147 Copynumber: 2.0 Consensus size: 153
1293054 TGTTATACTA
1293064 AAAATATGGAATGTCCTGAATTGGATGGTAAGAGAAAAGATTTGGGATTGAATTATAAAAATGTA
1 AAAATATGGAATGTCCTGAATTGGATGGTAAGAGAAAAGATTTGGGATTGAATTATAAAAATGTA
*
1293129 AAATATAAGATATCGATTAATAAAAGTTAAAATGTAG-T-GA-ATATA-T-ATTTTGGTCGGAAA
66 AAATATAAGATATCGATTAATAAAAGTTAAAATGTAGATCAATATATAGTAATTTTGGTCGGAAA
1293189 TGAGATTCTGGGTCCACCTTAAT
131 TGAGATTCTGGGTCCACCTTAAT
1293212 AAAA-ATGGAATGTCCTGAATTGGATGGTAAGAGAAAAGATTTGGGATTGAATTATAAAAATGTA
1 AAAATATGGAATGTCCTGAATTGGATGGTAAGAGAAAAGATTTGGGATTGAATTATAAAAATGTA
1293276 AAATATAAGATATCGATTAATAAAAGTTAAAATGTAGAATCCAATTATATAGGTAATTTTGGTCG
66 AAATATAAGATATCGATTAATAAAAGTTAAAATGTAG-AT-CAA-TATATA-GTAATTTTGGTCG
1293341 GAAATGAGATTCTGGGTCCACCTTAA
127 GAAATGAGATTCTGGGTCCACCTTAA
1293367 AGATGGCGGC
Statistics
Matches: 145, Mismatches: 1, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
147 97 0.67
148 4 0.03
149 1 0.01
151 1 0.01
153 5 0.03
155 1 0.01
156 36 0.25
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.31
Consensus pattern (153 bp):
AAAATATGGAATGTCCTGAATTGGATGGTAAGAGAAAAGATTTGGGATTGAATTATAAAAATGTA
AAATATAAGATATCGATTAATAAAAGTTAAAATGTAGATCAATATATAGTAATTTTGGTCGGAAA
TGAGATTCTGGGTCCACCTTAAT
Found at i:1294526 original size:17 final size:17
Alignment explanation
Indices: 1294500--1294534 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1294490 CTTACATCCA
1294500 CACCCACCTACTATCTT
1 CACCCACCTACTATCTT
*
1294517 CACCCGCCTACTATCTT
1 CACCCACCTACTATCTT
1294534 C
1 C
1294535 TAAACTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.49, G:0.03, T:0.29
Consensus pattern (17 bp):
CACCCACCTACTATCTT
Found at i:1296351 original size:57 final size:58
Alignment explanation
Indices: 1296258--1296371 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 58
1296248 CATAATCCAT
*
1296258 TTATATAAATAGTTAAAGGAAATATTATTATTTTTTGATAACTCGAATTCGACTAATC
1 TTATATAAATAGTTAAAGGAAATATTATTATTTTTTGATAACTCGAATTCGAATAATC
1296316 TTAT-TAAATAGTTAAAGGAAATATTATTATTTTTTGATAACTCGAATTCGAATAAT
1 TTATATAAATAGTTAAAGGAAATATTATTATTTTTTGATAACTCGAATTCGAATAAT
1296372 TATATTTATA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 51 0.93
58 4 0.07
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (58 bp):
TTATATAAATAGTTAAAGGAAATATTATTATTTTTTGATAACTCGAATTCGAATAATC
Found at i:1296979 original size:2 final size:2
Alignment explanation
Indices: 1296972--1297002 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1296962 ATACATTATT
1296972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1297003 GGATGGCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1298808 original size:15 final size:15
Alignment explanation
Indices: 1298766--1298801 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1298756 TCGAATATTC
1298766 AAAATACTAAAAATA
1 AAAATACTAAAAATA
1298781 AAAATACTAAAAATA
1 AAAATACTAAAAATA
1298796 AAAATA
1 AAAATA
1298802 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATACTAAAAATA
Found at i:1304665 original size:39 final size:39
Alignment explanation
Indices: 1304622--1304705 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
1304612 AGATTAGTAG
*
1304622 ATCCAGCAGTTGAGAAACTTTAGAGAGATTGATGTCCAA
1 ATCCAGCAGTTGAGAAACTTTAGAGAGATCGATGTCCAA
* * *
1304661 ATCCAACAGTTGAGAAGCTTTAGAGAGATCGATGTCCAG
1 ATCCAGCAGTTGAGAAACTTTAGAGAGATCGATGTCCAA
1304700 ATCCAG
1 ATCCAG
1304706 TGTAGAGCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (39 bp):
ATCCAGCAGTTGAGAAACTTTAGAGAGATCGATGTCCAA
Found at i:1310577 original size:163 final size:163
Alignment explanation
Indices: 1310296--1310615 Score: 453
Period size: 163 Copynumber: 2.0 Consensus size: 163
1310286 TATTATTAGC
* * * *
1310296 GATACGATAAGATGCAATTGTTGGCAAATATTAACAGGATAAGCAAGGATAGCAGTGCAATGAGA
1 GATACGATAAGATGCAATTATTGGCAAATATTAACAGGATAAGCAAGAATAGCAGCGCAAGGAGA
* *
1310361 TACTCAACCTTAGATGAAAAGCCATTTTCAAGCGTACAAGAGGTAACGATGAAGCCACTAATGGC
66 AACTCAACCTTAGATGAAAAGCCATTTTCAAGCGTACAAGAGGTAACGATGAAGCCACTAATAGC
**
1310426 AACTGTGATGCCATCGGCAGTTTCAAGCATAGG
131 AACCATGATGCCATCGGCAGTTTCAAGCATAGG
* *
1310459 GATATGATAAGATG-ATATTATTGGCAAATATTAACAGGATAAGCATGAATAGCAGCGCAAGGAG
1 GATACGATAAGATGCA-ATTATTGGCAAATATTAACAGGATAAGCAAGAATAGCAGCGCAAGGAG
* * * * ** * *
1310523 AAACTCGACCTTAGGTGAAAAGCCATTTTCAAGTGTACGAGAGGTATTGATGAAGCCGCTGATAG
65 AAACTCAACCTTAGATGAAAAGCCATTTTCAAGCGTACAAGAGGTAACGATGAAGCCACTAATAG
*
1310588 CAACCATGATGCCATCGGTAGTTTCAAG
130 CAACCATGATGCCATCGGCAGTTTCAAG
1310616 AGTGGTGGCA
Statistics
Matches: 137, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
162 1 0.01
163 136 0.99
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (163 bp):
GATACGATAAGATGCAATTATTGGCAAATATTAACAGGATAAGCAAGAATAGCAGCGCAAGGAGA
AACTCAACCTTAGATGAAAAGCCATTTTCAAGCGTACAAGAGGTAACGATGAAGCCACTAATAGC
AACCATGATGCCATCGGCAGTTTCAAGCATAGG
Found at i:1313094 original size:18 final size:18
Alignment explanation
Indices: 1313071--1313106 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1313061 AATTAGAAAC
1313071 AATGATGATAACTAACCT
1 AATGATGATAACTAACCT
1313089 AATGATGATAACTAACCT
1 AATGATGATAACTAACCT
1313107 TCTCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
AATGATGATAACTAACCT
Found at i:1318213 original size:6 final size:6
Alignment explanation
Indices: 1318204--1318269 Score: 60
Period size: 6 Copynumber: 10.0 Consensus size: 6
1318194 ATTGGCACTA
* *
1318204 AAATTT AAATTT TACTTT AAATTT AAATTACT AAAATTT AAATTT AAATTACT
1 AAATTT AAATTT AAATTT AAATTT AAATT--T -AAATTT AAATTT AAATT--T
1318257 AAAATTT AAATTT
1 -AAATTT AAATTT
1318270 TGTTTTAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 36 0.72
7 2 0.04
8 2 0.04
9 10 0.20
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:1318245 original size:21 final size:21
Alignment explanation
Indices: 1318219--1318269 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1318209 TAAATTTTAC
1318219 TTTAAATTTAAATTACTAAAA
1 TTTAAATTTAAATTACTAAAA
1318240 TTTAAATTTAAATTACTAAAA
1 TTTAAATTTAAATTACTAAAA
1318261 TTTAAATTT
1 TTTAAATTT
1318270 TGTTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATTTAAATTACTAAAA
Found at i:1321827 original size:17 final size:18
Alignment explanation
Indices: 1321796--1321829 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1321786 TTTAAAATAA
1321796 TATATTTTATAATAATTT
1 TATATTTTATAATAATTT
1321814 TATATTTT-TAATAATT
1 TATATTTTATAATAATT
1321830 AAAGAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTATAATAATTT
Found at i:1322511 original size:16 final size:17
Alignment explanation
Indices: 1322490--1322524 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1322480 AACATATTAT
1322490 TTCGGGTCGGGTT-GGG
1 TTCGGGTCGGGTTCGGG
*
1322506 TTCGGGTTGGGTTCGGG
1 TTCGGGTCGGGTTCGGG
1322523 TT
1 TT
1322525 TTATCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.11, G:0.51, T:0.37
Consensus pattern (17 bp):
TTCGGGTCGGGTTCGGG
Found at i:1322512 original size:11 final size:11
Alignment explanation
Indices: 1322496--1322524 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1322486 TTATTTCGGG
1322496 TCGGGTTGGGT
1 TCGGGTTGGGT
1322507 TCGGGTTGGGT
1 TCGGGTTGGGT
1322518 TCGGGTT
1 TCGGGTT
1322525 TTATCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.52, T:0.38
Consensus pattern (11 bp):
TCGGGTTGGGT
Found at i:1324393 original size:183 final size:185
Alignment explanation
Indices: 1324069--1324436 Score: 679
Period size: 183 Copynumber: 2.0 Consensus size: 185
1324059 TACTTGTAGA
1324069 TATTAGTTTCCCCCATTTTCAAGCCATCACCCCAATCAAAATTAGGAAATGTAGACGGTATAATT
1 TATTAGTTTCCCCCATTTTCAAGCCATCACCCCAATCAAAATTAGGAAATGTAGACGGTATAATT
*
1324134 TCGTGGATTTCGCACTTTACCTGCTCCAATTGAAACGAGAATGGGTATAAGTTTAGTGGGTAGTG
66 TCATGGATTTCGCACTTTACCTGCTCCAATTGAAACGAGAATGGGTATAAGTTTAGTGGGTAGTG
*
1324199 GGCGTGTGTGGATATAAAAAAGTCATACACACAGTGAGAAGTGGGTAATTGATGG
131 GGCGGGTGTGGATATAAAAAAGTCATACACACAGTGAGAAGTGGGTAATTGATGG
1324254 TATTAGTTT-CCCCATTTTCAAGCCATCA-CCCAATCAAAATTAGG-AATGTAGACGGGTATAAT
1 TATTAGTTTCCCCCATTTTCAAGCCATCACCCCAATCAAAATTAGGAAATGTAGAC-GGTATAAT
*
1324316 TTCATGGATTTCGCACTTTACCTGCTCCAATTGAAGCGAGAATGGGTATAAGTTTAGTGGGTAGT
65 TTCATGGATTTCGCACTTTACCTGCTCCAATTGAAACGAGAATGGGTATAAGTTTAGTGGGTAGT
1324381 GGGCGGGTGTGGATATAAAAAAGTCATACACACAGTGAGAAGTGGGTAATTGATGG
130 GGGCGGGTGTGGATATAAAAAAGTCATACACACAGTGAGAAGTGGGTAATTGATGG
1324437 GTTTGAGACC
Statistics
Matches: 179, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
182 9 0.05
183 142 0.79
184 19 0.11
185 9 0.05
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (185 bp):
TATTAGTTTCCCCCATTTTCAAGCCATCACCCCAATCAAAATTAGGAAATGTAGACGGTATAATT
TCATGGATTTCGCACTTTACCTGCTCCAATTGAAACGAGAATGGGTATAAGTTTAGTGGGTAGTG
GGCGGGTGTGGATATAAAAAAGTCATACACACAGTGAGAAGTGGGTAATTGATGG
Found at i:1326418 original size:64 final size:63
Alignment explanation
Indices: 1326281--1326438 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 63
1326271 AATTGTTCAG
* * * *
1326281 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAATATCGGATGCAATT
1 TGTGTATCGATGCATAGGGAGTGCATCGATACACCCCTTAAAAATGAAAACATCGGATGC-ATT
* * * * *
1326345 AGTGCATCGATGCATAGGGAGTGCATCGATACACCCCCTT-AAGATTAAAACATCGAAGGTGC-T
1 TGTGTATCGATGCATAGGGAGTGCATCGATACA-CCCCTTAAAAATGAAAACATCG--GATGCAT
1326408 T
63 T
*
1326409 TGTGTATCGATTCAT-GGGTAGTGCATCGAT
1 TGTGTATCGATGCATAGGG-AGTGCATCGAT
1326439 GCACATGTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
63 3 0.04
64 65 0.83
65 6 0.08
66 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (63 bp):
TGTGTATCGATGCATAGGGAGTGCATCGATACACCCCTTAAAAATGAAAACATCGGATGCATT
Found at i:1327369 original size:2 final size:2
Alignment explanation
Indices: 1327362--1327404 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1327352 GATTAGATTA
1327362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1327404 A
1 A
1327405 GTGAAATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1327575 original size:2 final size:2
Alignment explanation
Indices: 1327568--1327599 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1327558 TAGGTAAATG
1327568 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1327600 GATTATGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1328155 original size:23 final size:23
Alignment explanation
Indices: 1328111--1328155 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1328101 CATTTTATAT
* *
1328111 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTACAATTATACGC
* *
1328134 GGCACTTCGGTATATTTATACG
1 GGCACTTCGGTACAATTATACG
1328156 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTACAATTATACGC
Found at i:1330853 original size:14 final size:13
Alignment explanation
Indices: 1330826--1330851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1330816 GTCAATTGAC
1330826 AAGTAAGATTTTT
1 AAGTAAGATTTTT
1330839 AAGTAAGATTTTT
1 AAGTAAGATTTTT
1330852 TATTTATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AAGTAAGATTTTT
Found at i:1334164 original size:2 final size:2
Alignment explanation
Indices: 1334152--1334223 Score: 85
Period size: 2 Copynumber: 37.0 Consensus size: 2
1334142 ATCCAGTAAG
* * *
1334152 TA TA TA CA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1334194 TA TA CA TA CA TA TA -A TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1334224 CATACACATA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1334170 original size:4 final size:4
Alignment explanation
Indices: 1334155--1334365 Score: 236
Period size: 4 Copynumber: 53.5 Consensus size: 4
1334145 CAGTAAGTAT
* * * * * * *
1334155 ATAC ATAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
1334203 ATATA ATAT ATAT ATATT ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC
1 ATA-C ATAC ATAC ATA-C ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1334251 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC AT-- ATAC ATAC ATTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC
*
1334298 ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1334344 ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC AT
1334366 GTCATCATTT
Statistics
Matches: 187, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
2 6 0.03
4 170 0.91
5 11 0.06
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAC
Found at i:1334731 original size:31 final size:31
Alignment explanation
Indices: 1334693--1334762 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1334683 CCTCGGCAAT
*
1334693 TGTCCATAGGTTCCAAAGAACCTAGGTAAAC
1 TGTCCATAGGTTCCAAAGAACATAGGTAAAC
* *** *
1334724 TGTCCATATGTTCTTTAGAACATAGGTATAC
1 TGTCCATAGGTTCCAAAGAACATAGGTAAAC
1334755 TGTCCATA
1 TGTCCATA
1334763 TGCCCCGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (31 bp):
TGTCCATAGGTTCCAAAGAACATAGGTAAAC
Found at i:1338666 original size:4 final size:4
Alignment explanation
Indices: 1338659--1338683 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1338649 ATCCAGTAAG
1338659 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
1338684 GTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1343152 original size:4 final size:4
Alignment explanation
Indices: 1343143--1343182 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
1343133 AGCTATTAAT
*
1343143 TTTA TTTA TTTA TATA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1343183 CTTGAGTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1345632 original size:124 final size:128
Alignment explanation
Indices: 1345484--1345739 Score: 484
Period size: 124 Copynumber: 2.0 Consensus size: 128
1345474 TGTTGGTTGA
1345484 TTTTTAGTTTAGGGTTTATGTTTTTTTTTTTTGCATACATCAGTGGCATTGTAAAAAATCATTTA
1 TTTTTAGTTTAGGGTTTATGTTTTTTTTTTTTGCATACATCAGTGGCATTGTAAAAAATCATTTA
1345549 TATAAAGCATATATAAATTCTTCACT-GTC-TTTTAC-CAAAATTGCTTTCTTTGA-TTTATT
66 TATAAAGCATATATAAATTCTTCACTGGTCATTTTACACAAAATTGCTTTCTTTGATTTTATT
1345608 TTTTTAGTTTAGGGTTTATGTTTTTTTTTTTTGCATACATCAGTGGCATTGTAAAAAATCATTTA
1 TTTTTAGTTTAGGGTTTATGTTTTTTTTTTTTGCATACATCAGTGGCATTGTAAAAAATCATTTA
1345673 TATAAAGCATATATAAATTCTTCACTGGTCATTTTACACAAAATTGCTTTCTTTGATTTTATT
66 TATAAAGCATATATAAATTCTTCACTGGTCATTTTACACAAAATTGCTTTCTTTGATTTTATT
1345736 TTTT
1 TTTT
1345740 ATACTGTCTT
Statistics
Matches: 128, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
124 91 0.71
125 3 0.02
126 6 0.05
127 18 0.14
128 10 0.08
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (128 bp):
TTTTTAGTTTAGGGTTTATGTTTTTTTTTTTTGCATACATCAGTGGCATTGTAAAAAATCATTTA
TATAAAGCATATATAAATTCTTCACTGGTCATTTTACACAAAATTGCTTTCTTTGATTTTATT
Found at i:1349237 original size:2 final size:2
Alignment explanation
Indices: 1349230--1349267 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1349220 ATCACCATTA
1349230 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1349268 AGTGAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1351588 original size:4 final size:4
Alignment explanation
Indices: 1351581--1351608 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1351571 CAAGTTCGTT
1351581 CATG CATG CATG CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG
1351609 TATGAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:1351934 original size:19 final size:21
Alignment explanation
Indices: 1351898--1351940 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
1351888 AGGGTAAAAT
*
1351898 AATTTTGAAATTAGAAATGAA
1 AATTTTGAAATTAGAAATAAA
*
1351919 AATTTT-AATTTA-AAATAAA
1 AATTTTGAAATTAGAAATAAA
1351938 AAT
1 AAT
1351941 AGTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
AATTTTGAAATTAGAAATAAA
Found at i:1352725 original size:19 final size:19
Alignment explanation
Indices: 1352691--1352766 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
1352681 TTCGGTTTGC
*
1352691 AAAAAAACCGGTTTTTTTA
1 AAAAAAACCGGATTTTTTA
*
1352710 AAAAAAACCTGATTTTTTCGGA
1 AAAAAAACCGGATTTTTT---A
* * *
1352732 TAAAAATCC-AATTTTTT-
1 AAAAAAACCGGATTTTTTA
*
1352749 TAAAAAACCGGATTTTTT
1 AAAAAAACCGGATTTTTT
1352767 TCGGATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.17
18 7 0.15
19 16 0.35
21 7 0.15
22 8 0.17
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (19 bp):
AAAAAAACCGGATTTTTTA
Found at i:1352763 original size:39 final size:41
Alignment explanation
Indices: 1352692--1352788 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 41
1352682 TCGGTTTGCA
** *
1352692 AAAAAACCGGTTTTTTTAAAAAAAACCTGA-TTTTTTCGGAT
1 AAAAAACCAATTTTTTT-AAAAAAACCGGATTTTTTTCGGAT
*
1352733 AAAAATCCAATTTTTTT-AAAAAACCGGATTTTTTTCGGAT
1 AAAAAACCAATTTTTTTAAAAAAACCGGATTTTTTTCGGAT
*
1352773 AAAAAACCAGTTTTTT
1 AAAAAACCAATTTTTT
1352789 ATCCGGTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 10 0.20
40 25 0.51
41 14 0.29
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (41 bp):
AAAAAACCAATTTTTTTAAAAAAACCGGATTTTTTTCGGAT
Found at i:1352789 original size:39 final size:38
Alignment explanation
Indices: 1352692--1352789 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 38
1352682 TCGGTTTGCA
* *
1352692 AAAAAACCGGTTTTTTTAAAAAAAACCTGATTTTTTCGGAT
1 AAAAAACCAG-TTTTTT--AAAAAACCGGATTTTTTCGGAT
* *
1352733 AAAAATCCAATTTTTTTAAAAAACCGGATTTTTTTCGGAT
1 AAAAAACC-AGTTTTTTAAAAAACCGGA-TTTTTTCGGAT
1352773 AAAAAACCAGTTTTTTA
1 AAAAAACCAGTTTTTTA
1352790 TCCGGTTTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.37
40 18 0.37
41 13 0.27
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (38 bp):
AAAAAACCAGTTTTTTAAAAAACCGGATTTTTTCGGAT
Found at i:1352807 original size:27 final size:24
Alignment explanation
Indices: 1352773--1352834 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
1352763 TTTTTCGGAT
*
1352773 AAAAAACCAGTTTTTTATCCGGTTTGA
1 AAAAAACCAGTTTTTAATCCGG--T-A
1352800 AAAAAACC-GATTTTTAATCCGGTA
1 AAAAAACCAG-TTTTTAATCCGGTA
1352824 AAAAAACCAGT
1 AAAAAACCAGT
1352835 CGTTCAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 10 0.31
25 2 0.06
26 1 0.03
27 19 0.59
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (24 bp):
AAAAAACCAGTTTTTAATCCGGTA
Found at i:1360056 original size:143 final size:142
Alignment explanation
Indices: 1359799--1360076 Score: 448
Period size: 143 Copynumber: 2.0 Consensus size: 142
1359789 TATAAGAGAA
* *
1359799 ATTAGGTTGTTTATAAATATAATAATATTTAAAAAATAAATTTTAAAAACATCAGATTATGACAC
1 ATTAGGTTATTTATAAATATAATAATATTTAAAAAATAAATTTTAAAAACACCAGATTATGACAC
* * * * *
1359864 GTGTCACTTGACTGGATAAATTAATGTTGTTGATGACTTATACACCTAAATGAGTAACGTTTGTA
66 GTGTCACTTAACTGGATAAATTAACGTTATTGATGACCTAGACACCTAAATGAGTAACGTTTGTA
1359929 ATGTTGGCAGAT
131 ATGTTGGCAGAT
* *
1359941 ATTAGGTTATTTATAAATATAATAATATTTAAAAAAATAAATTTTAAAATCACCAGATTGTGACA
1 ATTAGGTTATTTATAAATATAATAATATTT-AAAAAATAAATTTTAAAAACACCAGATTATGACA
* *
1360006 CGTGTCACTTAACTGGATAAATTAACGTTATTGATGACCTGGACACCTAAATGATTAACGTTTGT
65 CGTGTCACTTAACTGGATAAATTAACGTTATTGATGACCTAGACACCTAAATGAGTAACGTTTGT
1360071 AATGTT
130 AATGTT
1360077 AGCACCTGGA
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 29 0.23
143 95 0.77
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (142 bp):
ATTAGGTTATTTATAAATATAATAATATTTAAAAAATAAATTTTAAAAACACCAGATTATGACAC
GTGTCACTTAACTGGATAAATTAACGTTATTGATGACCTAGACACCTAAATGAGTAACGTTTGTA
ATGTTGGCAGAT
Found at i:1362434 original size:20 final size:20
Alignment explanation
Indices: 1362406--1362446 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1362396 TGGTTTTCCA
* *
1362406 AAATTTATTTTTGAAATTAT
1 AAATATATTTTTGAAACTAT
1362426 AAATATATTTTTGAAACTAT
1 AAATATATTTTTGAAACTAT
1362446 A
1 A
1362447 TTGAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
AAATATATTTTTGAAACTAT
Found at i:1362662 original size:25 final size:25
Alignment explanation
Indices: 1362611--1362662 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1362601 ATTCATTTTT
* **
1362611 TTAAAAATAATTATAATTTTATGAA
1 TTAAAAATAACTATAAAGTTATGAA
1362636 TTAAAAACTAACTATAAAGTTAT-AA
1 TTAAAAA-TAACTATAAAGTTATGAA
1362661 TT
1 TT
1362663 TTTTAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TTAAAAATAACTATAAAGTTATGAA
Found at i:1362669 original size:22 final size:22
Alignment explanation
Indices: 1362644--1362690 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1362634 AATTAAAAAC
1362644 TAACTATAAAGTTATAATTTTT
1 TAACTATAAAGTTATAATTTTT
*
1362666 TAACTATAAAGTTGTAATTTTT
1 TAACTATAAAGTTATAATTTTT
1362688 TAA
1 TAA
1362691 AAACACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (22 bp):
TAACTATAAAGTTATAATTTTT
Found at i:1363958 original size:34 final size:35
Alignment explanation
Indices: 1363875--1363962 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 35
1363865 TCGGGTTAGG
*
1363875 TTTTTTAAGTGTAATATTCGAGTCGGTTCGGGTTC
1 TTTTTTAAGTGTGATATTCGAGTCGGTTCGGGTTC
*** *
1363910 GGGTTTAGGT-TGATATTCGAGTCAGG-TCGGGTT-
1 TTTTTTAAGTGTGATATTCGAGTC-GGTTCGGGTTC
1363943 TTTTTTAAGTGTGATATTCG
1 TTTTTTAAGTGTGATATTCG
1363963 GGTATAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
33 6 0.14
34 28 0.67
35 8 0.19
ACGTcount: A:0.17, C:0.09, G:0.30, T:0.44
Consensus pattern (35 bp):
TTTTTTAAGTGTGATATTCGAGTCGGTTCGGGTTC
Found at i:1365218 original size:60 final size:59
Alignment explanation
Indices: 1365143--1365322 Score: 182
Period size: 60 Copynumber: 3.0 Consensus size: 59
1365133 AAATATGCAT
* * * *
1365143 ATTTTGGGATGAAATTGGAATGTTAAAAAAGTTTGGGATCAAATTAGAATGAATGTCATA
1 ATTTAGGGATGAAATTGAAATATT-AAAAAGTTTGGGATCAATTTAGAATGAATGTCATA
* * * *
1365203 ATTTAGGGATGAAATTGAAATATTCAAAAGTTTGATGATTAGTTTAGAATG-ATAGTCATA
1 ATTTAGGGATGAAATTGAAATATTAAAAAGTTTG-GGATCAATTTAGAATGAAT-GTCATA
* * * * * * *
1365263 GTTTAGAGATGAAATTAAAATATTTAAAAGTTTAAGGATCAATTTAAAATGAGTGTCATA
1 ATTTAGGGATGAAATTGAAATATTAAAAAGTTT-GGGATCAATTTAGAATGAATGTCATA
1365323 TTTTGGAGAA
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
59 11 0.11
60 86 0.88
61 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (59 bp):
ATTTAGGGATGAAATTGAAATATTAAAAAGTTTGGGATCAATTTAGAATGAATGTCATA
Found at i:1373896 original size:18 final size:18
Alignment explanation
Indices: 1373840--1373897 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
1373830 AAGATTTACA
*
1373840 TTTGAGAGATTTACTGT-
1 TTTGAGAGATTTACCGTG
*
1373857 TTTGATG-GATTTTCTCGTG
1 TTTGA-GAGATTTAC-CGTG
*
1373876 TTTGAGAGATTTACGGTG
1 TTTGAGAGATTTACCGTG
1373894 TTTG
1 TTTG
1373898 TTAAAAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 11 0.33
18 11 0.33
19 11 0.33
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (18 bp):
TTTGAGAGATTTACCGTG
Found at i:1377414 original size:23 final size:23
Alignment explanation
Indices: 1377394--1377476 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
1377384 TGAATTCTAT
*
1377394 TATCATATTGACCTGGATTCTGA
1 TATCATATTGACATGGATTCTGA
* *
1377417 TCTGATATTGACATGGATTCTGA
1 TATCATATTGACATGGATTCTGA
* * *
1377440 TCTGATACATGACATGGATTCTGA
1 TATCATA-TTGACATGGATTCTGA
*
1377464 TATGATACTTGAC
1 TATCATA-TTGAC
1377477 TTGAATTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 27 0.51
24 26 0.49
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (23 bp):
TATCATATTGACATGGATTCTGA
Found at i:1377457 original size:24 final size:24
Alignment explanation
Indices: 1377401--1377476 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
1377391 TATTATCATA
*
1377401 TTGACCTGGATTCTGATCTGATA-
1 TTGACATGGATTCTGATCTGATAC
1377424 TTGACATGGATTCTGATCTGATAC
1 TTGACATGGATTCTGATCTGATAC
* *
1377448 ATGACATGGATTCTGATATGATAC
1 TTGACATGGATTCTGATCTGATAC
1377472 TTGAC
1 TTGAC
1377477 TTGAATTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 22 0.46
24 26 0.54
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TTGACATGGATTCTGATCTGATAC
Found at i:1377601 original size:35 final size:35
Alignment explanation
Indices: 1377554--1377628 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
1377544 TGGAGGAAGA
*
1377554 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
*
1377589 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGTC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1377624 TTACT
1 TTACT
1377629 GTTCGCGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.35
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:1382590 original size:25 final size:24
Alignment explanation
Indices: 1382561--1382617 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1382551 ATTATTTTAT
1382561 TATTTAAAT-ATATATTTTAGAAAAA
1 TATTTAAATGATA-ATTTT-GAAAAA
* * *
1382586 TATTTAAGTGATAATTTTTAAAGA
1 TATTTAAATGATAATTTTGAAAAA
1382610 TATTTAAA
1 TATTTAAA
1382618 ACGACAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 11 0.41
25 13 0.48
26 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
TATTTAAATGATAATTTTGAAAAA
Found at i:1385818 original size:18 final size:18
Alignment explanation
Indices: 1385762--1385819 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
1385752 AAGATTTACA
*
1385762 TTTGAGAGATTTACTGT-
1 TTTGAGAGATTTACCGTG
*
1385779 TTTGATG-GATTTTCTCGTG
1 TTTGA-GAGATTTAC-CGTG
*
1385798 TTTGAGAGATTTACGGTG
1 TTTGAGAGATTTACCGTG
1385816 TTTG
1 TTTG
1385820 TTAAAAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 11 0.33
18 11 0.33
19 11 0.33
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (18 bp):
TTTGAGAGATTTACCGTG
Found at i:1389338 original size:23 final size:23
Alignment explanation
Indices: 1389318--1389400 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
1389308 TGAATTCTAT
*
1389318 TATCATATTGACCTGGATTCTGA
1 TATCATATTGACATGGATTCTGA
*
1389341 TATGATATTGACATGGATTCTGA
1 TATCATATTGACATGGATTCTGA
* * *
1389364 TCTGATACATGACATGGATTCTGA
1 TATCATA-TTGACATGGATTCTGA
*
1389388 TATGATACTTGAC
1 TATCATA-TTGAC
1389401 TTGAATTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 27 0.51
24 26 0.49
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (23 bp):
TATCATATTGACATGGATTCTGA
Found at i:1389381 original size:24 final size:24
Alignment explanation
Indices: 1389325--1389400 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
1389315 TATTATCATA
*
1389325 TTGACCTGGATTCTGATATGATA-
1 TTGACATGGATTCTGATATGATAC
*
1389348 TTGACATGGATTCTGATCTGATAC
1 TTGACATGGATTCTGATATGATAC
*
1389372 ATGACATGGATTCTGATATGATAC
1 TTGACATGGATTCTGATATGATAC
1389396 TTGAC
1 TTGAC
1389401 TTGAATTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 21 0.45
24 26 0.55
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (24 bp):
TTGACATGGATTCTGATATGATAC
Found at i:1389525 original size:35 final size:35
Alignment explanation
Indices: 1389478--1389552 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1389468 TGGAGGAAGA
*
1389478 TTACTTGGAGGCTCATCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
* *
1389513 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGTC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
1389548 TTACT
1 TTACT
1389553 GTTCGCGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.11, C:0.27, G:0.28, T:0.35
Consensus pattern (35 bp):
TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
Found at i:1393347 original size:25 final size:24
Alignment explanation
Indices: 1393318--1393374 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1393308 ATTATTTTAT
1393318 TATTTAAAT-ATATATTTTAGAAAAA
1 TATTTAAATGATA-ATTTT-GAAAAA
* * *
1393343 TATTTAAGTGATAATTTTTAAAGA
1 TATTTAAATGATAATTTTGAAAAA
1393367 TATTTAAA
1 TATTTAAA
1393375 ACGACAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 11 0.41
25 13 0.48
26 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
TATTTAAATGATAATTTTGAAAAA
Found at i:1400841 original size:29 final size:28
Alignment explanation
Indices: 1400809--1400898 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
1400799 ATGAAAATGA
1400809 AATGTTCAAAAGTTTGAGGATTAATTTAG
1 AATGTTCAAAAGTTT-AGGATTAATTTAG
* * * *
1400838 AATGAGTC-ATAGTTTAGAGATGAAATTAG
1 AATG-TTCAAAAGTTTAG-GATTAATTTAG
* *
1400867 AATGTTTAAAAGTTTAGGGACTAATTTAG
1 AATGTTCAAAAGTTTA-GGATTAATTTAG
1400896 AAT
1 AAT
1400899 AATCCATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
28 3 0.06
29 41 0.87
30 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (28 bp):
AATGTTCAAAAGTTTAGGATTAATTTAG
Found at i:1400878 original size:58 final size:60
Alignment explanation
Indices: 1400738--1400898 Score: 181
Period size: 58 Copynumber: 2.7 Consensus size: 60
1400728 TATATACGGA
*
1400738 ATGAAATTCA-AATGTTCAAAAAGTTTGGGGATTAATTTAGAATGGAGGTCATAGGTTGAGT
1 ATGAAATT-AGAATGTT-AAAAAGTTTGAGGATTAATTTAGAATGGAGGTCATAGGTTGAGT
* * *
1400799 ATGAAAAT-GAAATGTTCAAAAGTTTGAGGATTAATTTAGAAT-GA-GTCATAGTTTAGAG-
1 ATGAAATTAG-AATGTTAAAAAGTTTGAGGATTAATTTAGAATGGAGGTCATAGGTT-GAGT
* *
1400857 ATGAAATTAGAATGTTTAAAAGTTT-AGGGACTAATTTAGAAT
1 ATGAAATTAGAATGTTAAAAAGTTTGA-GGATTAATTTAGAAT
1400899 AATCCATAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 44 0.50
59 6 0.07
60 24 0.27
61 13 0.15
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.34
Consensus pattern (60 bp):
ATGAAATTAGAATGTTAAAAAGTTTGAGGATTAATTTAGAATGGAGGTCATAGGTTGAGT
Found at i:1405619 original size:45 final size:45
Alignment explanation
Indices: 1405564--1405651 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
1405554 GGCAATGTTG
* *
1405564 GTGATTGTTGTGGTTGCGGCTTTGGTTTAGTCATTGGTGGTGGTT
1 GTGATGGTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGGTT
* *
1405609 GTGATGGTTGTGGTTGTGGGTTTGATTTAGTCATTGGTGGTGG
1 GTGATGGTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGG
1405652 CGGCGGCGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.08, C:0.05, G:0.42, T:0.45
Consensus pattern (45 bp):
GTGATGGTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGGTT
Found at i:1405663 original size:45 final size:45
Alignment explanation
Indices: 1405570--1405664 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
1405560 GTTGGTGATT
* ** * *
1405570 GTTGTGGTTGCGGCTTTGGTTTAGTCATTGGTGGTGGTTGTGATG
1 GTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGGCGGCGACG
* * *
1405615 GTTGTGGTTGTGGGTTTGATTTAGTCATTGGTGGTGGCGGCGGCG
1 GTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGGCGGCGACG
1405660 GTTGT
1 GTTGT
1405665 AATGGGTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.06, C:0.07, G:0.44, T:0.42
Consensus pattern (45 bp):
GTTGTGGTTGCGGCTTTGATTTAGTCATTGGTGGTGGCGGCGACG
Found at i:1407061 original size:14 final size:15
Alignment explanation
Indices: 1407035--1407063 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1407025 TGAGGATTTT
1407035 TTTTAGTTTATTCTA
1 TTTTAGTTTATTCTA
1407050 TTTTAG-TTATTCTA
1 TTTTAGTTTATTCTA
1407064 ATAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTTAGTTTATTCTA
Found at i:1408948 original size:25 final size:26
Alignment explanation
Indices: 1408887--1408949 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1408877 TTATTTTATT
1408887 TATTAAAAT-ATAATTTTTAGAAAAA
1 TATTAAAATGATAATTTTTAGAAAAA
* * *
1408912 TATTCAACTGATAATTTTT--AAAGA
1 TATTAAAATGATAATTTTTAGAAAAA
1408936 TATTTAAAATGATA
1 TA-TTAAAATGATA
1408950 GTTAAGATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 6 0.19
25 16 0.52
26 9 0.29
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (26 bp):
TATTAAAATGATAATTTTTAGAAAAA
Found at i:1409007 original size:37 final size:38
Alignment explanation
Indices: 1408931--1409008 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
1408921 GATAATTTTT
* * * *
1408931 AAAGATATTTAAAATGATAGTTAAGATATAATATGTAA
1 AAAGATATTTAAAATAATAGTTAAGAAAAAATATATAA
*
1408969 AAAGATTTTTAAAATAATA-TTAAGAAAAAA-ATAATAA
1 AAAGATATTTAAAATAATAGTTAAGAAAAAATAT-ATAA
1409006 AAA
1 AAA
1409009 TTCTTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 2 0.06
37 15 0.44
38 17 0.50
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (38 bp):
AAAGATATTTAAAATAATAGTTAAGAAAAAATATATAA
Found at i:1421097 original size:15 final size:15
Alignment explanation
Indices: 1421077--1421109 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1421067 TTAACTAGGT
*
1421077 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
1421092 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
1421107 GGG
1 GGG
1421110 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:1427092 original size:36 final size:36
Alignment explanation
Indices: 1427051--1427124 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
1427041 ATTAAACGGA
*
1427051 GACGAGGAAAAACTGTTTATGCTAAACGGGGACAGG
1 GACGAGGAAAAACCGTTTATGCTAAACGGGGACAGG
*
1427087 GACGAGGAAAAACCGTTTATGTTAAACGGGGACAGG
1 GACGAGGAAAAACCGTTTATGCTAAACGGGGACAGG
1427123 GA
1 GA
1427125 TGGGTTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.34, T:0.16
Consensus pattern (36 bp):
GACGAGGAAAAACCGTTTATGCTAAACGGGGACAGG
Found at i:1428831 original size:2 final size:2
Alignment explanation
Indices: 1428824--1428850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1428814 CTTCGTGGGC
1428824 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1428851 ATAAATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1429578 original size:2 final size:2
Alignment explanation
Indices: 1429571--1429597 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1429561 TGTAATTTAT
1429571 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1429598 GTATGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1437675 original size:21 final size:21
Alignment explanation
Indices: 1437645--1437684 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1437635 AATTAGTTAA
*
1437645 AAAATTAATGATAAATTATTT
1 AAAATAAATGATAAATTATTT
*
1437666 AAAATAAATGATAAGTTAT
1 AAAATAAATGATAAATTAT
1437685 ATCAATGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAATAAATGATAAATTATTT
Found at i:1438203 original size:20 final size:20
Alignment explanation
Indices: 1438165--1438203 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1438155 TTTCAATTGA
*
1438165 ATTAAAGTAAATTTCAAAAC
1 ATTAAAGTAAATTGCAAAAC
* *
1438185 ATTAAATTAAATTGGAAAA
1 ATTAAAGTAAATTGCAAAA
1438204 TATGTAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
ATTAAAGTAAATTGCAAAAC
Found at i:1440217 original size:15 final size:15
Alignment explanation
Indices: 1440185--1440214 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1440175 AATAATTAAC
1440185 ATAATATATTTTATA
1 ATAATATATTTTATA
1440200 ATAATATA-TTTATA
1 ATAATATATTTTATA
1440214 A
1 A
1440215 ATATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATATATTTTATA
Found at i:1440268 original size:12 final size:12
Alignment explanation
Indices: 1440245--1440269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1440235 ATTAAATTAA
1440245 TATATTTTATAT
1 TATATTTTATAT
1440257 TATATTTTATAT
1 TATATTTTATAT
1440269 T
1 T
1440270 TTCAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:1440298 original size:20 final size:22
Alignment explanation
Indices: 1440267--1440309 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1440257 TATATTTTAT
*
1440267 ATTTTCAATAAT-TAAATATAA
1 ATTTTCAATAATATAAAAATAA
1440288 ATTTT-AATAATATAAAAATAA
1 ATTTTCAATAATATAAAAATAA
1440309 A
1 A
1440310 AATTCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTTCAATAATATAAAAATAA
Found at i:1440755 original size:42 final size:42
Alignment explanation
Indices: 1440708--1440792 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1440698 AAAAAATATT
*
1440708 TAAATTAAAAATAAATTAAA-TTAAAAAAGCCCTCCAATGATA
1 TAAATTAAAAATAAATTAAATTTAAAAAA-CCCTCCAATAATA
*
1440750 TAAATTAAACATAAATTAAATTTAAAAAACCCTCCAATAATA
1 TAAATTAAAAATAAATTAAATTTAAAAAACCCTCCAATAATA
1440792 T
1 T
1440793 TGTCACACGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 32 0.80
43 8 0.20
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.28
Consensus pattern (42 bp):
TAAATTAAAAATAAATTAAATTTAAAAAACCCTCCAATAATA
Found at i:1441827 original size:2 final size:2
Alignment explanation
Indices: 1441820--1441859 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1441810 GTACCTGGTT
1441820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1441860 TAAATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1441944 original size:39 final size:38
Alignment explanation
Indices: 1441891--1441992 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 38
1441881 ATTCTCAATT
1441891 TATTTCAC-TCTAACATTCTAAATTCCTAATTTCTTAAA
1 TATTTCACAT-TAACATTCTAAATTCCTAATTTCTTAAA
**
1441929 -ATTTGCCACCA-TAACATTCTAAATTTTTAATTTCTTAAA
1 TATTT--CA-CATTAACATTCTAAATTCCTAATTTCTTAAA
1441968 TTATTTCACATTAACATTCTAAATT
1 -TATTTCACATTAACATTCTAAATT
1441993 AATTTTTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
37 4 0.07
38 2 0.04
39 44 0.80
40 1 0.02
41 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (38 bp):
TATTTCACATTAACATTCTAAATTCCTAATTTCTTAAA
Found at i:1450625 original size:20 final size:20
Alignment explanation
Indices: 1450581--1450898 Score: 174
Period size: 20 Copynumber: 15.6 Consensus size: 20
1450571 AATGACCAAT
* * *
1450581 AAAATCACAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1450600 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1450620 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1450640 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1450660 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1450681 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1450704 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1450724 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1450744 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1450764 AGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1450787 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1450807 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1450827 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1450847 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1450867 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1450887 AAAATCGCAACG
1 AAAATCGCAACG
1450899 TTAAAAAGAA
Statistics
Matches: 241, Mismatches: 46, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.07
20 182 0.76
21 14 0.06
23 29 0.12
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Done.